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Abstract

Motivation: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to many alternative and subsequent versions. Taken together, the underlying changes reflect a model’s provenance and thus can give valuable insights into the studied biology. Currently, however, changes cannot be semantically interpreted. To improve this situation, we developed an ontology of terms describing changes in computational biology models. The ontology can be used by scientists and within software to characterise model updates at the level of single changes. When studying or reusing a model, these annotations help with determining the relevance of a change in a given context.

Methods: We manually studied changes in selected models from BioModels and the Physiome Model Repository. Using the BiVeS tool for difference detection, we then performed an automatic analysis of changes in all models published in

these repositories. The resulting set of concepts led us to define candidate terms for the ontology. In a final step, we aggregated and classified these terms and built the first version of the ontology.

Results: We present COMODI, an ontology needed because COmputational MOdels DIffer. It empowers users and software to describe changes in a model on the semantic level. COMODI also enables software to implement user-specific filter options for the display of model changes. Finally, COMODI is the next step towards predicting how a change in a model influences the simulation study.

Conclusion: COMODI, coupled with our algorithm for difference detection, ensures the transparency of a model’s evolution and it enhances the traceability of updates and error corrections.

Availability: COMODI is encoded in OWL. It is openly available at http://comodi.sems.uni-rostock.de/.

Author Comment

This is a preprint submission before submitting it to Journal of Biomedical Semantics.

Supplemental Information

COMODI: Additional Information

Example COMBINE Archive of annotated differences

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Martin Scharm conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, developed software, created initial version of the ontology, and created the website.

Dagmar Waltemath conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, created initial version of the ontology.

Pedro Mendes analyzed the data, wrote the paper, reviewed drafts of the paper.

Data Deposition

The Onltology and further resources https://github.com/SemsProject/COMODI

JAVA library https://github.com/binfalse/jCOMODI

Funding

This work has been funded by the German Federal Ministry of Education and Research (BMBF) as part
of the e:Bio program SEMS, FKZ 031 6194. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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